setwd('/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/new_celfile')
library(affy)
library(frmaTools)
library(frma)
data<-ReadAffy()
setwd('/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/')
dat<-read.table("output_batch.txt",header=FALSE)
vec<-as.vector(dat[,2])
vectors<-makeVectors(data, vec, verbose=TRUE)
setwd('/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/samplefiles/in1')
data<-ReadAffy()
k1<-frma(data, background="rma", normalize="quantile", summarize="robust_weighted_average", vectors)
write.exprs(k1,file="1.txt",sep="\t")

setwd('/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/TCGA_frma')
data<-ReadAffy()
k1<-frma(data, background="rma", normalize="quantile", summarize="robust_weighted_average", vectors)
write.exprs(k1,file="frma_custom_cdf.txt",sep="\t")
q()
